Contacts of the strand formed by residues 276 - 282 (chain D) in PDB entry 1OIK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 276 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D GLN* 3.8 33.4 - - + +
96D LEU 3.7 2.5 - - - -
97D ASP* 4.4 12.6 - - + -
126D VAL* 3.0 37.2 + - + -
127D VAL* 2.9 47.8 + - + +
274D PRO* 5.1 6.1 - - + -
275D ARG* 1.3 81.1 - - - +
277D VAL* 1.3 67.0 + - - +
278D ARG* 4.2 10.5 - - - +
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Residues in contact with VAL 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D GLN* 3.6 1.4 - - - +
96D LEU* 3.0 52.3 + - + +
123D LEU* 3.6 26.7 - - + -
124D ARG 3.3 13.5 - - - +
125D SER* 4.2 12.8 - - - +
126D VAL 4.4 0.4 - - - +
127D VAL 5.1 0.4 - - - +
249D TRP* 5.4 5.4 - - + -
275D ARG* 3.9 36.1 - - + +
276D ILE* 1.3 80.1 - - - +
278D ARG* 1.3 66.6 + - - +
279D ARG 4.4 0.2 + - - -
1300D AKG 4.1 7.0 - - + +
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Residues in contact with ARG 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ASP* 3.0 36.8 + - - -
68D GLN* 2.8 27.8 + - - +
87D VAL* 4.1 11.4 - - + +
93D LEU* 3.9 20.4 - - + -
94D LEU 3.3 7.9 - - - +
95D GLN* 2.9 33.0 + - + -
123D LEU* 3.8 1.8 - - - -
124D ARG* 2.9 31.2 + - - +
126D VAL* 4.1 29.7 - - + +
276D ILE* 4.2 8.9 - - - +
277D VAL* 1.3 78.6 - - - +
279D ARG* 1.3 61.6 + - - +
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Residues in contact with ARG 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D HIS* 4.3 12.7 - - - +
92D TYR 3.9 1.4 - - - +
93D LEU* 3.6 3.1 - - - +
94D LEU* 2.8 74.2 + - + +
110D ASP* 3.0 11.2 + - - -
111D VAL* 5.0 2.6 - - - +
121D SER* 3.5 25.1 + - - -
122D ILE 3.2 6.5 - - - +
123D LEU* 3.4 21.7 - - + +
257D TRP* 5.7 0.2 - - + -
278D ARG* 1.3 74.3 - - - +
280D VAL* 1.3 62.3 + - - +
281D THR* 4.0 24.1 + - - +
1300D AKG 2.6 41.2 + - - +
1301D C26 2.7 34.2 + - - +
1302D FE2 3.6 0.2 - - - -
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Residues in contact with VAL 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D GLN* 3.8 17.9 - - + +
69D GLU* 4.3 16.2 - - + -
72D ALA* 3.6 26.2 - - + -
78D PRO* 4.0 17.3 - - + -
92D TYR* 4.5 10.8 - - + -
93D LEU* 3.4 29.8 - - + +
121D SER* 3.4 1.4 - - - -
122D ILE* 2.9 38.6 + - + +
279D ARG* 1.3 74.9 - - - +
281D THR* 1.3 73.6 + - - +
282D LEU* 4.3 1.7 + - + -
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Residues in contact with THR 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D PRO* 3.3 5.4 - - - +
79D VAL* 2.9 57.9 + - + +
80D ALA 5.0 2.0 - - - +
81D HIS* 5.1 6.5 - - - -
92D TYR 5.0 1.8 + - - -
110D ASP* 5.1 0.9 + - - +
118D PRO* 3.6 22.6 - - + +
120D ALA 3.6 6.7 + - - -
121D SER* 2.8 19.9 + - - -
279D ARG* 4.0 21.5 + - - +
280D VAL* 1.3 77.4 - - - +
282D LEU* 1.3 59.3 + - - +
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Residues in contact with LEU 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D ALA* 3.8 21.8 - - + +
75D LEU* 3.7 32.8 - - + +
76D GLY* 3.9 8.3 - - - +
77D GLU 3.6 4.7 - - - +
78D PRO* 3.7 30.3 - - + -
79D VAL* 4.2 2.7 - - - -
118D PRO* 3.1 5.5 - - - +
119D LYS* 2.9 40.6 + - + -
120D ALA* 3.0 25.6 + - + +
122D ILE* 4.0 17.0 - - + -
280D VAL* 4.4 1.6 - - + -
281D THR* 1.3 76.5 - - - +
283D ALA* 1.3 66.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il